Mercurial > repos > yating-l > hubarchivecreator
changeset 72:2440ce10848b draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit a60f8496cccf4c5a07ba7d75876198eda997f07d
| author | yating-l |
|---|---|
| date | Wed, 27 Sep 2017 15:34:20 -0400 |
| parents | b724e559907e |
| children | 3de7eb63604d |
| files | TrackDb.py TrackDb.pyc datatypes/Datatype.py datatypes/Datatype.pyc datatypes/binary/BigBed.py datatypes/binary/BigBed.pyc datatypes/binary/BigWig.py datatypes/binary/BigWig.pyc datatypes/interval/Bed.py datatypes/interval/Bed.pyc datatypes/interval/BedBlastAlignments.py datatypes/interval/BedSimpleRepeats.pyc datatypes/interval/Interval.py datatypes/interval/Interval.pyc hubArchiveCreator.xml macros.xml |
| diffstat | 16 files changed, 30 insertions(+), 16 deletions(-) [+] |
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--- a/TrackDb.py Wed Sep 27 11:15:44 2017 -0400 +++ b/TrackDb.py Wed Sep 27 15:34:20 2017 -0400 @@ -67,7 +67,7 @@ if not "color" in extraSettings: extraSettings["color"] = "#000000" extraSettings["color"] = TrackDb.getRgb(extraSettings["color"]) - if not "group" in extraSettings: + if not "group" in extraSettings or not extraSettings["group"]: extraSettings["group"] = "Default group" if not "thickDrawItem" in extraSettings: extraSettings["thickDrawItem"] = "off"
--- a/datatypes/Datatype.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/Datatype.py Wed Sep 27 15:34:20 2017 -0400 @@ -75,7 +75,7 @@ def validateData(self): """validate the input data with DataValidation""" - def initSettings(self, trackType = None): + def initSettings(self): #Initialize required fields: trackName, longLabel, shortLable self.trackName = self.trackSettings["name"] if self.trackSettings["long_label"]: @@ -87,8 +87,7 @@ else: self.shortLabel = self.trackSettings["short_label"] self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) - if trackType: - self.trackType = trackType + @abc.abstractmethod def createTrack(self):
--- a/datatypes/binary/BigBed.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/binary/BigBed.py Wed Sep 27 15:34:20 2017 -0400 @@ -16,8 +16,8 @@ super(BigBed, self).__init__() self.inputFile = input_bigbed_path self.trackSettings = data_bigbed - self.dataType = self._determine_track_type(self.inputFile) - self.trackType = self.dataType + self.trackType = self._determine_track_type(self.inputFile) + self.dataType = self.trackType.replace(' ', '') self.seqType = None def initSettings(self): @@ -65,7 +65,7 @@ if match: extra_mark = "." if match.group(1) == match.group(2) else "+" - bed_type = "bigBed%s%s" % (match.group(1), extra_mark) + bed_type = "bigBed %s %s" % (match.group(1), extra_mark) break cmd_ph.wait()
--- a/datatypes/binary/BigWig.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/binary/BigWig.py Wed Sep 27 15:34:20 2017 -0400 @@ -17,12 +17,12 @@ self.inputFile = input_bigwig_path self.trackSettings = data_bigwig self.dataType = "bigWig" + self.trackType=self._determine_track_type(self.inputFile) def initSettings(self): super(BigWig, self).initSettings() self.trackName = "".join( ( self.trackName, ".bigwig" ) ) self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) - self.trackType=self._determine_track_type(self.inputFile) if "track_color" in self.trackSettings: self.extraSettings["color"] = self.trackSettings["track_color"] if "group_name" in self.trackSettings:
--- a/datatypes/interval/Bed.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/interval/Bed.py Wed Sep 27 15:34:20 2017 -0400 @@ -2,6 +2,7 @@ import os import tempfile +import logging # Internal dependencies from Interval import Interval @@ -13,13 +14,14 @@ super(Bed, self).__init__() self.inputFile = inputBedGeneric self.trackSettings = data_bed_generic - self.trackType = "bigBed" - self.dataType = "bed" self.bedFields = None self.extFields = None + self.dataType = "bed" + def initSettings(self): - super(Bed, self).initSettings(trackType = self.trackType) + super(Bed, self).initSettings() + self.trackType = self._determine_track_type() self.trackName = "".join( ( self.trackName, ".bb") ) self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName) if "track_color" in self.trackSettings: @@ -40,7 +42,7 @@ self.validator = DataValidation(self.inputFile, self.getValidateType(), self.chromSizesFile.name) self.validator.validate() - def getBedFields(self): + def _getBedFields(self): """count number of bed fields for generic bed format""" with open(self.inputFile, 'r') as bed: l = bed.readline().split() @@ -48,9 +50,21 @@ def getValidateType(self): if not self.bedFields: - return self.dataType + str(self.getBedFields()) + logging.debug("bedFields is not defined, consider the file as Bed generic format, datatype = bed%s", str(self.bedFields)) + self.bedFields = self._getBedFields() + return self.dataType + str(self.bedFields) elif not self.extFields: return self.dataType + str(self.bedFields) else: return self.dataType + str(self.bedFields) + "+" + str(self.extFields) + def _determine_track_type(self): + if not self.bedFields: + return "bigBed" + else: + if not self.extFields: + extra_mark = "." + else: + extra_mark = "+" + return "bigBed %s %s" % (str(self.bedFields), extra_mark) +
--- a/datatypes/interval/BedBlastAlignments.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/interval/BedBlastAlignments.py Wed Sep 27 15:34:20 2017 -0400 @@ -13,4 +13,5 @@ super(BedBlastAlignments, self).__init__(input_bed_blast_alignments_false_path, data_bed_blast_alignments) self.seqType = 2 + self.trackType = "bigBed 12 +"
--- a/datatypes/interval/Interval.py Wed Sep 27 11:15:44 2017 -0400 +++ b/datatypes/interval/Interval.py Wed Sep 27 15:34:20 2017 -0400 @@ -21,7 +21,7 @@ super(Interval, self).__init__() def getConvertType(self): - return (self.dataType.lower(), self.trackType.lower()) + return (self.dataType.lower(), self.trackType.split()[0].lower()) def getValidateOptions(self, tab=None, autoSql=None): options = dict()
--- a/hubArchiveCreator.xml Wed Sep 27 11:15:44 2017 -0400 +++ b/hubArchiveCreator.xml Wed Sep 27 15:34:20 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2"> +<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0"> <description> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization.
--- a/macros.xml Wed Sep 27 11:15:44 2017 -0400 +++ b/macros.xml Wed Sep 27 15:34:20 2017 -0400 @@ -17,7 +17,7 @@ <!-- description.html --> <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/> <!-- trackDb.txt --> - <extra_files type="file" name="myHub/@GENOME@/trackDb.txt" value="@TEST@/myHub/@GENOME@/trackDb.txt"> + <extra_files type="file" name="myHub/@GENOME@/trackDb.txt"> <assert_contents> <has_text text="track"/> <has_text text="longLabel"/>